Direct Observation of the Double-Stranded DNA Formation through Metal Ion-Mediated Base Pairing in the Nanoscale Structure

This work demonstrates single-molecule imaging of metal-ion induced double-stranded DNA formation in DNA nanostructures. The formation of the metal ion-mediated base pairing in a DNA origami frame was examined using C-Ag-C and T-Hg-T metallo-base pairs. The target DNA strands containing consecutive C or T were incorporated into the DNA frame, and the binding was controlled by the addition of metal ions. Double-stranded DNA formation was monitored by observing the structural changes in the incorporated DNA strands using high-speed atomic force microscopy (AFM). Using the T-Hg-T base pair, the dynamic formation of unique dsDNA and its dissociation were observed. The formation of an unusual shape of dsDNA with consecutive T-Hg-T base pairs was visualized in the designed nanoscale structure.     

Direct Observation of Dynamic Interactions between Orientation-Controlled Nucleosomes in a DNA Origami Frame

The nucleosome is one of the most fundamental units involved in gene expression and consequent cell development, differentiation, and expression of cell functions. We report here a method to place reconstituted nucleosomes into a DNA origami frame for direct observation using high-speed atomic-force microscopy (HS-AFM). By using this method, multiple nucleosomes can be incorporated into a DNA origami frame and real-time movement of nucleosomes can be visualized. The arrangement and conformation of nucleosomes and the distance between two nucleosomes can be designed and controlled. In addition, four nucleosomes can be placed in a DNA frame. Multiple nucleosomes were well accessible in each conformation. Dynamic movement of the individual nucleosomes were precisely monitored in the DNA frame, and their assembly and interaction were directly observed. Neither mica surface modification nor chemical fixation of nucleosomes is used in this method, meaning that the DNA frame not only holds nucleosomes, but also retains their natural state. This method offers a promising platform for investigating nucleosome interactions and for studying chromatin structure.     

Development of TfOH-Catalyzed Spirocyclization by Intramolecular Friedel-Crafts-type 1,4-Addition: Application to the Total Synthesis of the Unusual Proaporphine Alkaloid (±)-Misrametine

An effective method was developed for TfOH-catalyzed construction of spiroindanes and spirotetralines containing an all-carbon quaternary stereocenter. Intramolecular Friedel-Crafts-type 1,4-addition of the substrates which were di- or trimethoxybenzene and 2-cyclohexenone linked by an alkyl chain proceeded smoothly in the presence of 30 mol % of TfOH. A variety of spiroindanes and spirotetralines were obtained with moderate to excellent yield by this method. The reaction was successfully applied in the first total synthesis of the unusual proaporphine alkaloid (±)-misrametine, which included the gram-scale spirocyclization and selective O-demethylation used KCN in DMSO condition as key steps.     

Structural phase transitions in KCdF3 and K0.5Rb0.5CdF3

Successive structural transitions of KCdF₃ and K_0.5Rb_0.5CdF₃ have been studied by means of thermal diffusivity, polarized light scattering and X-ray diffraction. It is found that transitions occur at about 460 K and 475 K in KCdF₃, and at 222 K, 232 K, 250 K, 258 K and 268 K in K_0.5Rb_0.5CdF₃. The partial exchange between K⁺ and Rb⁺ ions gives rise to simultaneous condensation of the M^z ₃ and R^x ₂₅ soft phonons.     

Electronic States near the Fermi Level in the Antiferromagnetic and Ferromagnetic Spinels of Zn 1− x Cu x Cr 2 Se 4 ; 0.0 ≤ x ≤ 1.0

The electronic states of normal-type spinels in Zn 1 m x Cu x Cr 2 Se 4 have been studied by X-ray absorption spectroscopy near the K-edge of Zn, Cu, Cr and Se ions. It is found that characteristic white lines occur near the X-ray absorption threshold for Zn and Se ions, but not for Cu and Cr ions. It is also found that the white lines show a slight energy shift, which depends on the Cu concentration. The energy shifts mean that Fermi level gradually approaches the top region of the valence band of Se 2 m , on increasing the Cu ions. The substitution of Zn 2+ with Cu 1+ ions increases the number of positive carriers, holes. The holes occupying the top region of the valence band strongly correlate with Cr 4+ , which forms an empty orbital in the 3d-band of Cr 3+ and exchanges the valence electrons with Cr 3+ . It is interpreted that the ferromagnetism in Zn 1 m x Cu x Cr 2 Se 4 is made by double-exchange interaction between Cr 3+ and Cr 4+ ions and that holes contribute to the electronic conductivity of Zn 1 m x Cu x Cr 2 Se 4 .     

Reaction kinetics of dye decomposition processes monitored inside a photocatalytic microreactor

The photocatalytic decomposition processes of several kinds of dyes were monitored in real-time, in a TiO(2)-immobilized microcapillary. Their fluorescence spectra were measured directly from the UV-irradiated area. The photocatalytic reactions proceeded two orders of magnitude faster in the microcapillary than in a bulk reaction, and intermediate species were easily observed, due to their high concentrations compared with those of the reactants. Even for molecules that were not originally fluorescent, fluorescence was detected for the reactants or intermediate species of all the molecules studied. Photocatalytic reactions are typically analyzed in terms of pseudo-first-order or Langmuir-Hinshelwood reaction mechanisms, but it was ascertained that all of the dyes investigated in this study decomposed via a multi-step reaction such as a simple multi-step reaction, a self-catalytic reaction, and further, a more complicated reaction, depending on the molecular structure. These reactions were simulated using models based on the reaction kinetics, and reaction mechanisms were assigned to each type of dye. The fact that intermediate species (which are difficult to observe using conventional analytical methods) were successfully detected meant that mechanisms for different dyes could be further clarified.     

Topochemical synthesis and catalysis of metal nanoparticles exposed on crystalline cellulose nanofibers

Topochemical synthesis of gold nanoparticles (AuNPs) was achieved on crystalline cellulose single nanofibers (CSNFs), which were tailored from native cellulose. Exposed AuNPs@CSNFs composite exhibited an excellent catalytic efficiency: the turnover frequency of the AuNPs@CSNFs was up to 840 times that of conventional polymer-supported AuNPs, for a model aqueous reduction reaction. Our novel strategy provides a promising solution to realize efficient use of limited noble metals using natural bioresources.     

Photo-cross-linking-assisted thermal stability of DNA origami structures and its application for higher-temperature self-assembly

Heat tolerance of DNA origami structures has been improved about 30 °C by photo-cross-linking of 8-methoxypsoralen. To demonstrate one of its applications, the cross-linked origami were used for higher-temperature self-assembly, which markedly increased the yield of the assembled product when compared to the self-assembly of non-cross-linked origami at lower-temperature. By contrast, at higher-temperature annealing, native non-cross-linked tiles did not self-assemble to yield the desired product; however, they formed a nonspecific broken structure.     

Aggregation modeling of calcium carbonate particles by Monte Carlo simulation

The mechanism on aggregation of spindle granular particles of calcite was investigated for the carbonation of calcium hydroxide in aqueous suspension for the purpose of controlling morphology of CaCO₃. The experimental carbonation process was carried out in a semi-batch bubble column reactor under different conditions. Although, fine rhombic nano-particles diameter ranged from 100 to 200 nm were obtained at 291 K, a higher temperature of 300 K provided spindle granular particles with a length of 1.0–1.5 μm and a width of 0.3–0.5 μm. The average crystallite size was 28 nm for the fine rhombic nano-particles and 43 nm for the spindle granules. Zeta potential measurement for the spindle granules indicated that the suspension tended to be aggregated during the carbonation process. The effect of the degree of particle aggregation on the shape of the obtained calcite particles was studied by Monte Carlo simulations. Our simulation results elucidated the dependence of aggregation on unit particles, i.e., primary particles, on the experiment carbonation condition where the spindle granules were formed out of the unit particles under the same condition as the experiments. In addition, the formation mechanism of the granules was investigated by applying classical nucleation theory to the present simulations.     

A nonequilibrium temperature and fluctuation theorem for soft-mode turbulence

Non-thermal Brownian motion of a particle for soft-mode turbulence (SMT) in the electroconvection of a nematic liquid crystal has been experimentally investigated to clarify the statistical and thermodynamical aspects of SMT, using the Lagrangian picture in hydrodynamics. The effective temperature for SMT is obtained in two different ways based on the Einstein relation and the fluctuation theorem from the diffusion due to non-thermal particle fluctuations. The temperatures from the two methods agree well and exhibit a high value of 10⁶ K. They depend on the coarse-graining time, which reflects the anomalous properties of the macroscopic fluctuations for the SMT.